The impact of two tillage systems (conventional and no-tillage) on cereal contamination with fungi and Fusarium mycotoxins was investigated. Samples of soil, cereal seeds, seedlings and freshly harvested grain were taken from plots of an agricultural cooperative in Lithuania. All samples were subjected to mycological analyses. Grain samples were also used for analysis of mycotoxins. In the soil under no-tillage, contamination with fungal spores was 92.9% higher compared to the soil under conventional tillage. In the soil of the no-tillage system we found 20 fungal genera, while in the soil under conventional tillage the number of genera was 15% lower. On cereal seedlings in the no-tillage system fungal spore content was 24.6% higher (P>0.05) and detection frequency of Fusarium fungi was 22.9% higher (P>0.05) than on seedlings in the conventional system. During harvest in feeding grain grown in the conventional tillage system, 2.2-8.0 log₁₀ CFU g^‑1 fungal spores were detected, compared to 2.5‑12.0 log₁₀ CFU g^-1 in grain in the no-tillage system. A significantly higher grain contamination with Fusarium spp. was detected in the no-tillage system. However, the deoxynivalenol, zearalenone and T‑2 toxin content of grain was not considerably influenced by the different tillage systems, although it varied between species.